PIGC

gene
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Also known as PIG-CGPI2

Summary

PIGC (phosphatidylinositol glycan anchor biosynthesis class C, HGNC:8960) is a protein-coding gene on chromosome 1q24.3, encoding Phosphatidylinositol N-acetylglucosaminyltransferase subunit C (Q92535). Part of the glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex that catalyzes the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol and participates in the first step of GPI biosynthesis.

This gene encodes an endoplasmic reticulum associated protein that is involved in glycosylphosphatidylinositol (GPI) lipid anchor biosynthesis. The GPI lipid anchor is a glycolipid found on many blood cells and serves to anchor proteins to the cell surface. The encoded protein is one subunit of the GPI N-acetylglucosaminyl (GlcNAc) transferase that transfers GlcNAc to phosphatidylinositol (PI) on the cytoplasmic side of the endoplasmic reticulum. Two alternatively spliced transcripts that encode the same protein have been found for this gene. A pseudogene on chromosome 11 has also been characterized.

Source: NCBI Gene 5279 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): glycosylphosphatidylinositol biosynthesis defect 16 (Strong, GenCC) — +1 more curated relationship
  • GWAS associations: 80
  • Clinical variants (ClinVar): 6 total
  • Phenotypes (HPO): 8
  • MANE Select transcript: NM_153747

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:8960
Approved symbolPIGC
Namephosphatidylinositol glycan anchor biosynthesis class C
Location1q24.3
Locus typegene with protein product
StatusApproved
AliasesPIG-C, GPI2
Ensembl geneENSG00000135845
Ensembl biotypeprotein_coding
OMIM601730
Entrez5279

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 10 protein_coding, 5 protein_coding_CDS_not_defined

ENST00000344529, ENST00000367728, ENST00000465374, ENST00000475059, ENST00000478184, ENST00000484368, ENST00000489002, ENST00000862975, ENST00000862976, ENST00000862977, ENST00000862978, ENST00000934579, ENST00000934580, ENST00000952346, ENST00000952347

RefSeq mRNA: 2 — MANE Select: NM_153747 NM_002642, NM_153747

CCDS: CCDS1302

Canonical transcript exons

ENST00000344529 — 2 exons

ExonStartEnd
ENSE00001379751172441457172442830
ENSE00001909799172443988172444069

Expression profiles

Bgee: expression breadth ubiquitous, 288 present calls, max score 92.99.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.1234 / max 107.3570, expressed in 1799 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1591410.00911780
159153.84761632
159130.266782

Top tissues by expression

294 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
calcaneal tendonUBERON:000370192.99gold quality
skin of legUBERON:000151192.82gold quality
skin of abdomenUBERON:000141692.47gold quality
zone of skinUBERON:000001492.13gold quality
islet of LangerhansUBERON:000000692.12gold quality
monocyteCL:000057691.33gold quality
leukocyteCL:000073891.18gold quality
upper leg skinUBERON:000426291.16gold quality
mononuclear cellCL:000084291.15gold quality
body of pancreasUBERON:000115090.53gold quality
nippleUBERON:000203090.53gold quality
bone marrowUBERON:000237190.51gold quality
pancreasUBERON:000126490.33gold quality
hair follicleUBERON:000207390.13gold quality
body of uterusUBERON:000985390.02gold quality
right ovaryUBERON:000211889.92gold quality
palpebral conjunctivaUBERON:000181289.91gold quality
gall bladderUBERON:000211089.90gold quality
left ovaryUBERON:000211989.90gold quality
penisUBERON:000098989.88gold quality
upper arm skinUBERON:000426389.76gold quality
esophagus squamous epitheliumUBERON:000692089.69gold quality
descending thoracic aortaUBERON:000234589.66gold quality
pancreatic ductal cellCL:000207989.61gold quality
granulocyteCL:000009489.32gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099189.32gold quality
rectumUBERON:000105289.29gold quality
ovaryUBERON:000099289.24gold quality
muscle layer of sigmoid colonUBERON:003580589.24gold quality
bloodUBERON:000017889.21gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-MTAB-9467no1.79
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting PIGC, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-335-3P99.9373.364958
HSA-MIR-153-5P99.8973.866317
HSA-MIR-659-3P99.8570.691620
HSA-MIR-128399.6972.423009
HSA-MIR-397599.6265.97697
HSA-MIR-5007-3P99.5168.141242
HSA-MIR-148A-5P99.3068.271141
HSA-MIR-316899.0867.751384
HSA-MIR-4695-5P99.0664.871151
HSA-MIR-2355-5P98.8365.511589
HSA-MIR-2115-5P98.6668.071191
HSA-MIR-426698.5367.291035

Literature-anchored findings (GeneRIF, showing 2)

  • Genes within recently identified loci associated with waist-hip ratio (WHR) exhibit fat depot-specific mRNA expression, which correlates with obesity-related traits. Adipose tissue (AT) mRNA expression of 6 genes (TBX15/WARS2, STAB1, PIGC, ZNRF3, GRB14 (PMID:23670221)
  • PIGC joins the list of genes in which mutations result in defective biosynthesis of GPI anchoring, manifesting by global developmental delay and seizure disorder. (PMID:27694521)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriopigcENSDARG00000009113
mus_musculusPigcENSMUSG00000026698
rattus_norvegicusPigcENSRNOG00000026497
drosophila_melanogasterPIG-CFBGN0035435
caenorhabditis_elegansWBGENE00011860

Protein

Protein identifiers

Phosphatidylinositol N-acetylglucosaminyltransferase subunit CQ92535 (reviewed: Q92535)

Alternative names: Phosphatidylinositol-glycan biosynthesis class C protein

All UniProt accessions (1): Q92535

UniProt curated annotations — full annotation on UniProt →

Function. Part of the glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex that catalyzes the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol and participates in the first step of GPI biosynthesis.

Subunit / interactions. Component of the glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex composed at least by PIGA, PIGC, PIGH, PIGP, PIGQ, PIGY and DPM2. Interacts with PIGQ. Interacts with the heterodimer PIGA:PIGH.

Subcellular location. Endoplasmic reticulum membrane.

Disease relevance. Glycosylphosphatidylinositol biosynthesis defect 16 (GPIBD16) [MIM:617816] An autosomal recessive disorder characterized by delayed psychomotor development, intellectual disability, and seizures. The disease is caused by variants affecting the gene represented in this entry.

Pathway. Glycolipid biosynthesis; glycosylphosphatidylinositol-anchor biosynthesis.

Similarity. Belongs to the PIGC family.

RefSeq proteins (2): NP_002633, NP_714969* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR009450Plno_GlcNAc_GPI2Family

Pfam: PF06432

UniProt features (13 total): transmembrane region 8, sequence variant 4, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q92535-F188.980.63

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-162710Synthesis of glycosylphosphatidylinositol (GPI)

MSigDB gene sets: 158 (showing top): MORF_MTA1, BORCZUK_MALIGNANT_MESOTHELIOMA_UP, GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GOBP_PHOSPHATIDYLINOSITOL_METABOLIC_PROCESS, GOBP_GLYCOLIPID_BIOSYNTHETIC_PROCESS, REACTOME_SYNTHESIS_OF_GLYCOSYLPHOSPHATIDYLINOSITOL_GPI, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, MODULE_16, MORF_PSMC2, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, PATIL_LIVER_CANCER, GOBP_PHOSPHOLIPID_BIOSYNTHETIC_PROCESS

GO Biological Process (1): GPI anchor biosynthetic process (GO:0006506)

GO Molecular Function (2): catalytic activity (GO:0003824), protein binding (GO:0005515)

GO Cellular Component (4): glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506), endoplasmic reticulum membrane (GO:0005789), endoplasmic reticulum (GO:0005783), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Post-translational modification: synthesis of GPI-anchored proteins1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
GPI anchor metabolic process1
glycolipid biosynthetic process1
glycerophospholipid biosynthetic process1
GPI anchored protein biosynthesis1
molecular_function1
binding1
endoplasmic reticulum membrane1
membrane protein complex1
endoplasmic reticulum protein-containing complex1
transferase complex1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
cellular anatomical structure1

Protein interactions and networks

STRING

764 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PIGCPIGQQ9BRB3999
PIGCPIGHQ14442999
PIGCPIGAP37287999
PIGCPIGPP57054999
PIGCPIGYQ3MUY2999
PIGCDPM2O94777996
PIGCPYURFQ96I23840
PIGCERI1Q8IV48830
PIGCPIGBQ92521814
PIGCPIGLQ9Y2B2811
PIGCPIGGQ5H8A4811
PIGCPIGWQ7Z7B1807
PIGCPIGMQ9H3S5795
PIGCPIGOQ8TEQ8774
PIGCPIGKQ92643774
PIGCPIGVQ9NUD9774

IntAct

14 interactions, top by confidence:

ABTypeScore
PIGAPIGPpsi-mi:“MI:0914”(association)0.710
PIGADPM2psi-mi:“MI:0914”(association)0.660
DPM2PIGApsi-mi:“MI:0914”(association)0.660
PIGCPIGApsi-mi:“MI:0914”(association)0.640
PIGCPIGQpsi-mi:“MI:0915”(physical association)0.500
PIGCDPM2psi-mi:“MI:0915”(physical association)0.500
KLF10PIGCpsi-mi:“MI:0915”(physical association)0.370
PIGCPIGHpsi-mi:“MI:0914”(association)0.350
SLC4A8PSMA7psi-mi:“MI:0914”(association)0.350
PIGCZHX1psi-mi:“MI:0915”(physical association)0.000

BioGRID (16): ZHX1 (Two-hybrid), PIGC (Proximity Label-MS), PIGC (Proximity Label-MS), PIGC (Proximity Label-MS), PIGC (Proximity Label-MS), PIGC (Proximity Label-MS), PIGC (Proximity Label-MS), PIGC (Proximity Label-MS), PIGC (Negative Genetic), PIGC (Affinity Capture-Western), PIGC (Reconstituted Complex), PIGC (Proximity Label-MS), PIGC (Cross-Linking-MS (XL-MS)), PIGC (Affinity Capture-MS), PIGC (Affinity Capture-RNA)

ESM2 similar proteins: A1CKG4, A1D708, A2XSY1, A4R2N5, A6QRX6, A6RRF7, A7EMV1, B0XXU1, B2AR67, O46521, O95214, O95807, P13498, P52650, Q0CNZ5, Q0JDK9, Q0V0G4, Q17QF8, Q1E1E0, Q28F21, Q2GSS4, Q32PD8, Q39080, Q3ZBX1, Q4WXT2, Q566G2, Q5PQQ4, Q5R5Z8, Q5RDE9, Q61462, Q62737, Q6CC06, Q6GM42, Q6GPA8, Q6P0C7, Q6PDU4, Q7S693, Q8K3C0, Q8TAC9, Q92535

Diamond homologs: O59802, O64761, Q3ZBX1, Q54M40, Q5PQQ4, Q92535, Q9CXR4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

6 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance2
Likely benign0
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

985 predictions. Top by Δscore:

VariantEffectΔscore
1:172379014:TTAG:Tacceptor_loss1.0000
1:172379015:TAGGC:Tacceptor_loss1.0000
1:172379016:A:AGacceptor_gain1.0000
1:172379016:AG:Aacceptor_gain1.0000
1:172379016:AGG:Aacceptor_loss1.0000
1:172379016:AGGCT:Aacceptor_gain1.0000
1:172379017:G:Aacceptor_gain1.0000
1:172379017:G:GTacceptor_gain1.0000
1:172379017:GGC:Gacceptor_gain1.0000
1:172379017:GGCT:Gacceptor_gain1.0000
1:172379017:GGCTG:Gacceptor_gain1.0000
1:172379178:ATAAC:Adonor_gain1.0000
1:172379181:AC:Adonor_gain1.0000
1:172379183:G:GGdonor_gain1.0000
1:172387119:T:TAacceptor_gain1.0000
1:172387356:GCAG:Gdonor_gain1.0000
1:172387359:GGT:Gdonor_loss1.0000
1:172387360:G:GGdonor_gain1.0000
1:172387360:GTA:Gdonor_loss1.0000
1:172388569:TCA:Tacceptor_loss1.0000
1:172388571:A:Cacceptor_loss1.0000
1:172379179:TAAC:Tdonor_gain0.9900
1:172379180:AAC:Adonor_gain0.9900
1:172379180:AACG:Adonor_loss0.9900
1:172379181:ACGTA:Adonor_loss0.9900
1:172379182:CGTAA:Cdonor_loss0.9900
1:172379183:G:Adonor_loss0.9900
1:172379184:TAA:Tdonor_loss0.9900
1:172379185:A:AAdonor_loss0.9900
1:172379186:A:AAdonor_loss0.9900

AlphaMissense

1921 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:172441774:C:AW283C0.997
1:172441774:C:GW283C0.997
1:172441776:A:GW283R0.996
1:172441776:A:TW283R0.996
1:172442524:G:CF33L0.996
1:172442524:G:TF33L0.996
1:172442526:A:GF33L0.996
1:172441795:T:AK276N0.994
1:172441795:T:GK276N0.994
1:172441796:T:AK276I0.989
1:172441781:C:TG281E0.988
1:172442525:A:GF33S0.987
1:172441993:A:CF210L0.986
1:172441993:A:TF210L0.986
1:172441995:A:GF210L0.986
1:172442188:G:CS145R0.986
1:172442188:G:TS145R0.986
1:172442190:T:GS145R0.986
1:172442525:A:CF33C0.985
1:172442061:A:GC188R0.984
1:172441775:C:GW283S0.980
1:172441773:C:GD284H0.978
1:172441782:C:GG281R0.978
1:172441782:C:TG281R0.978
1:172441775:C:AW283L0.977
1:172441760:A:GI288T0.975
1:172441830:A:GC265R0.974
1:172442023:G:CF200L0.974
1:172442023:G:TF200L0.974
1:172442025:A:GF200L0.974

dbSNP variants (sampled 300 via entrez): RS1002071156 (1:172441413 C>G,T), RS1002495123 (1:172442604 T>A,C), RS1002618194 (1:172440991 T>C), RS1004016126 (1:172445649 G>A), RS1004172250 (1:172444820 C>T), RS1005469820 (1:172440965 C>T), RS1005560529 (1:172441687 T>G), RS1005940619 (1:172441402 T>C), RS1006310195 (1:172443433 T>A), RS1007693796 (1:172443508 C>G), RS1008734515 (1:172444923 G>C), RS1009119503 (1:172444530 A>C,G), RS1011604749 (1:172443754 T>C), RS1011827201 (1:172444160 G>A,C), RS1012919419 (1:172444436 T>C)

Disease associations

OMIM: gene MIM:601730 | disease phenotypes: MIM:617816

GenCC curated gene-disease

DiseaseClassificationInheritance
glycosylphosphatidylinositol biosynthesis defect 16StrongAutosomal recessive
autosomal recessive non-syndromic intellectual disabilitySupportiveAutosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
glycosylphosphatidylinositol biosynthesis defect 16LimitedAR

Mondo (2): glycosylphosphatidylinositol biosynthesis defect 16 (MONDO:0040500), autosomal recessive non-syndromic intellectual disability (MONDO:0019502)

Orphanet (0):

HPO phenotypes

8 total (8 of 8 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0001249Intellectual disability
HP:0001250Seizure
HP:0001263Global developmental delay
HP:0002465Poor speech
HP:0003155Elevated circulating alkaline phosphatase concentration
HP:0003593Infantile onset
HP:0031936Delayed ability to walk

GWAS associations

80 associations (top):

StudyTraitp-value
GCST000829_1Waist-hip ratio1.000000e-17
GCST002782_155Waist-to-hip ratio adjusted for body mass index2.000000e-10
GCST002782_156Waist-to-hip ratio adjusted for body mass index9.000000e-07
GCST002782_157Waist-to-hip ratio adjusted for body mass index4.000000e-15
GCST002782_158Waist-to-hip ratio adjusted for body mass index3.000000e-07
GCST002782_159Waist-to-hip ratio adjusted for body mass index9.000000e-11
GCST002782_160Waist-to-hip ratio adjusted for body mass index1.000000e-15
GCST003518_51Daytime sleep phenotypes3.000000e-06
GCST004064_61Waist-hip ratio7.000000e-08
GCST004064_70Waist-hip ratio1.000000e-08
GCST004505_35Waist-to-hip ratio adjusted for BMI (adjusted for smoking behaviour)1.000000e-11
GCST004505_36Waist-to-hip ratio adjusted for BMI (adjusted for smoking behaviour)9.000000e-15
GCST004507_22Waist-to-hip ratio adjusted for BMI (joint analysis main effects and smoking interaction)7.000000e-06
GCST004507_7Waist-to-hip ratio adjusted for BMI (joint analysis main effects and smoking interaction)9.000000e-06
GCST004567_114Waist-to-hip ratio adjusted for BMI (joint analysis for main effect and physical activity interaction)6.000000e-16
GCST004567_135Waist-to-hip ratio adjusted for BMI (joint analysis for main effect and physical activity interaction)1.000000e-14
GCST004567_36Waist-to-hip ratio adjusted for BMI (joint analysis for main effect and physical activity interaction)5.000000e-13
GCST004567_55Waist-to-hip ratio adjusted for BMI (joint analysis for main effect and physical activity interaction)3.000000e-13
GCST004576_54Waist-to-hip ratio adjusted for body mass index5.000000e-16
GCST004576_55Waist-to-hip ratio adjusted for body mass index6.000000e-14
GCST004576_56Waist-to-hip ratio adjusted for body mass index3.000000e-14
GCST004576_57Waist-to-hip ratio adjusted for body mass index5.000000e-16
GCST004578_103Waist-to-hip ratio adjusted for BMI in active individuals4.000000e-12
GCST004578_11Waist-to-hip ratio adjusted for BMI in active individuals3.000000e-12
GCST004578_112Waist-to-hip ratio adjusted for BMI in active individuals5.000000e-13
GCST004578_67Waist-to-hip ratio adjusted for BMI in active individuals8.000000e-14
GCST004578_86Waist-to-hip ratio adjusted for BMI in active individuals4.000000e-12
GCST010083_37Hemoglobin levels3.000000e-08
GCST012227_1164Hip circumference adjusted for BMI4.000000e-08
GCST012227_1165Hip circumference adjusted for BMI6.000000e-10

EFO canonical traits (10, from GWAS)

EFO IDTrait name
EFO:0004343waist-hip ratio
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0007828daytime rest measurement
EFO:0004318smoking behavior
EFO:0008002physical activity measurement
EFO:0004509hemoglobin measurement
EFO:0008039BMI-adjusted hip circumference
EFO:0010701mean reticulocyte volume
EFO:0004305erythrocyte count
EFO:0007789BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

33 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases methylation, affects expression, decreases expression3
sodium arsenitedecreases expression, increases abundance2
(+)-JQ1 compounddecreases expression2
Air Pollutantsaffects cotreatment, increases abundance, increases oxidation, decreases expression2
dicrotophosdecreases expression1
alpha-pineneincreases abundance, affects cotreatment, increases oxidation1
cobaltous chloridedecreases expression1
potassium chromate(VI)decreases expression1
methacrylaldehydeaffects cotreatment, increases oxidation, increases abundance1
cylindrospermopsinincreases expression1
CGP 52608affects binding, increases reaction1
abrinedecreases expression1
Acetaminophendecreases expression1
Acroleinaffects cotreatment, increases oxidation, increases abundance1
Arsenicdecreases expression, increases abundance1
Atrazinedecreases expression1
Cadmiumincreases expression1
Doxorubicindecreases expression1
Estradioldecreases expression1
Hydrogen Peroxideaffects cotreatment, increases expression1
Ozoneaffects cotreatment, increases oxidation, increases abundance1
Silicon Dioxidedecreases expression1
Smokedecreases expression1
Testosteronedecreases expression1
Tetrachlorodibenzodioxindecreases expression1
Theophyllineaffects cotreatment, increases expression1
Urethanedecreases expression1
Cyclosporineincreases expression1
Antirheumatic Agentsincreases expression1
Cadmium Chloridedecreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.